Flow Cytometry Standard I/O
Project description
FlowIO
Overview
FlowIO is a Python library for reading and writing Flow Cytometry Standard (FCS) files. Flow IO has zero external dependencies and works in both Python 2 and 3. For higher level interaction with flow cytometry data, including GatingML and FlowJo 10 support, see the related FlowKit project.
Installation
The recommended way to install FlowIO is via the pip
command:
pip install flowio
Or, if you prefer, you can install from the GitHub source:
git clone https://github.com/whitews/flowio
cd flowio
python setup.py install
Usage
FlowIO retrieves event data exactly as it is encoded in the FCS file: as a 1-dimensional list without separating the events into channels. However, all the metadata found within the FCS file is available as a dictionary via the 'text' attribute. Basic attributes are also available for commonly accessed properties. For example, the channel count can be used to easily convert the event data to a multi-column NumPy array:
import flowio
import numpy
fcs_data = flowio.FlowData('example.fcs')
npy_data = numpy.reshape(fcs_data.events, (-1, fcs_data.channel_count))
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